The selection, acquisition and use of high-quality, small-molecule libraries for screening are an essential aspect of drug discovery and chemical biology programs. Screening libraries continue to evolve as researchers gain a greater appreciation of the suitability of small molecules for specific biological targets, processes and environments. The decisions surrounding the make-up of any given small molecule library is informed by a multitude of variables, and opinions vary on best-practices. The fitness of any collection relies upon upfront filtering to avoid problematic compounds, assess appropriate physicochemical properties, install the ideal level of structural uniqueness and determine the desired extent of molecular complexity. These criteria are under constant evaluation and revision as academic and industrial organizations seek out collections that yield ever-improving results from their screening portfolios. Practical questions including cost, compound management, screening sophistication and assay objective also play a significant role in the choice of library composition. Our team continues to develop novel libraries including the Mechanism Interrogation Plate or MIPE and a novel stable metabolite library for use in both single agent and combination screening platforms. These libraries represent important tools for studying multiple models of disease.